Starting phenix.real_space_refine on Sat Mar 16 11:54:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eva_28624/03_2024/8eva_28624_neut_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 66 5.16 5 C 9514 2.51 5 N 2373 2.21 5 O 2634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B ASP 462": "OD1" <-> "OD2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B ASP 507": "OD1" <-> "OD2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 532": "OD1" <-> "OD2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 260": "OD1" <-> "OD2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 575": "OD1" <-> "OD2" Residue "C ASP 583": "OD1" <-> "OD2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C ASP 609": "OD1" <-> "OD2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ASP 461": "OD1" <-> "OD2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 484": "OE1" <-> "OE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 633": "OD1" <-> "OD2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14591 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 bond proxies already assigned to first conformer: 3692 Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3563 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 14, 'TRANS': 420} Chain breaks: 2 Chain: "C" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3681 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "D" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3579 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 12, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.50 Time building chain proxies: 9.40, per 1000 atoms: 0.64 Number of scatterers: 14591 At special positions: 0 Unit cell: (110.39, 107.07, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 4 15.00 O 2634 8.00 N 2373 7.00 C 9514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 3.3 seconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3358 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 9 sheets defined 59.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 167 through 192 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 195 through 198 No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 200 through 223 removed outlier: 3.987A pdb=" N ARG A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.948A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 298 through 328 Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 375 through 406 Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 488 through 497 Processing helix chain 'A' and resid 550 through 553 No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 593 through 607 Processing helix chain 'B' and resid 167 through 192 Proline residue: B 178 - end of helix removed outlier: 4.074A pdb=" N TYR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 222 Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 298 through 328 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 375 through 406 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 431 through 447 Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.440A pdb=" N LYS B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 477 removed outlier: 3.750A pdb=" N ILE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'B' and resid 592 through 610 Processing helix chain 'C' and resid 167 through 192 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 195 through 198 No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 200 through 223 removed outlier: 3.522A pdb=" N ARG C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 271 through 292 removed outlier: 4.634A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS C 280 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 281 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 291 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 328 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 375 through 406 Processing helix chain 'C' and resid 408 through 426 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 453 through 459 removed outlier: 5.529A pdb=" N SER C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 477 removed outlier: 5.754A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 550 through 553 No H-bonds generated for 'chain 'C' and resid 550 through 553' Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 593 through 608 Processing helix chain 'D' and resid 216 through 241 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 250 through 270 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 331 through 344 Processing helix chain 'D' and resid 348 through 378 Processing helix chain 'D' and resid 393 through 405 Processing helix chain 'D' and resid 417 through 448 removed outlier: 3.594A pdb=" N PHE D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 468 Processing helix chain 'D' and resid 473 through 490 Processing helix chain 'D' and resid 495 through 501 removed outlier: 4.413A pdb=" N THR D 501 " --> pdb=" O ASP D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 520 removed outlier: 3.938A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 525 No H-bonds generated for 'chain 'D' and resid 523 through 525' Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 621 through 628 Processing helix chain 'D' and resid 632 through 645 Processing sheet with id= A, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.598A pdb=" N ASP A 575 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.836A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 499 through 503 Processing sheet with id= D, first strand: chain 'B' and resid 527 through 530 removed outlier: 3.622A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 499 through 502 Processing sheet with id= F, first strand: chain 'C' and resid 539 through 541 removed outlier: 4.257A pdb=" N VAL C 539 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.090A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 560 through 564 Processing sheet with id= I, first strand: chain 'D' and resid 569 through 572 796 hydrogen bonds defined for protein. 2308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4442 1.34 - 1.46: 3247 1.46 - 1.58: 7147 1.58 - 1.70: 0 1.70 - 1.81: 105 Bond restraints: 14941 Sorted by residual: bond pdb=" C2' PCG D 901 " pdb=" C3' PCG D 901 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C2' PCG A 802 " pdb=" C3' PCG A 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C2' PCG C 802 " pdb=" C3' PCG C 802 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C2' PCG B 802 " pdb=" C3' PCG B 802 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " ideal model delta sigma weight residual 1.808 1.532 0.276 2.00e-02 2.50e+03 1.90e+02 ... (remaining 14936 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.93: 287 105.93 - 113.94: 8488 113.94 - 121.94: 8877 121.94 - 129.94: 2530 129.94 - 137.94: 102 Bond angle restraints: 20284 Sorted by residual: angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 112.23 128.19 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 128.11 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 112.23 128.09 -15.86 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 112.23 128.09 -15.86 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C2 PCG D 901 " pdb=" N3 PCG D 901 " pdb=" C4 PCG D 901 " ideal model delta sigma weight residual 120.18 106.86 13.32 3.00e+00 1.11e-01 1.97e+01 ... (remaining 20279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 7661 18.03 - 36.06: 947 36.06 - 54.09: 201 54.09 - 72.11: 37 72.11 - 90.14: 13 Dihedral angle restraints: 8859 sinusoidal: 3637 harmonic: 5222 Sorted by residual: dihedral pdb=" CA ASP A 193 " pdb=" C ASP A 193 " pdb=" N GLU A 194 " pdb=" CA GLU A 194 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA SER D 212 " pdb=" C SER D 212 " pdb=" N TYR D 213 " pdb=" CA TYR D 213 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASP D 286 " pdb=" C ASP D 286 " pdb=" N SER D 287 " pdb=" CA SER D 287 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 8856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2297 0.336 - 0.672: 8 0.672 - 1.007: 0 1.007 - 1.343: 0 1.343 - 1.679: 4 Chirality restraints: 2309 Sorted by residual: chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.05e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.05e+01 chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.05e+01 ... (remaining 2306 not shown) Planarity restraints: 2494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO D 273 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 369 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 370 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 502 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO D 503 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 503 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 503 " 0.037 5.00e-02 4.00e+02 ... (remaining 2491 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2655 2.77 - 3.30: 13485 3.30 - 3.83: 25232 3.83 - 4.37: 28335 4.37 - 4.90: 49084 Nonbonded interactions: 118791 Sorted by model distance: nonbonded pdb=" O MET C 585 " pdb=" OG1 THR C 589 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASP D 529 " pdb=" OG SER D 634 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR A 259 " pdb=" O VAL A 273 " model vdw 2.315 2.440 nonbonded pdb=" O ASP C 514 " pdb=" N ARG C 564 " model vdw 2.324 2.520 nonbonded pdb=" ND2 ASN A 317 " pdb=" OD1 ASP A 384 " model vdw 2.334 2.520 ... (remaining 118786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 609 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 609 or resid 801 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 609 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.010 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.790 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.369 14941 Z= 0.831 Angle : 1.044 15.956 20284 Z= 0.510 Chirality : 0.095 1.679 2309 Planarity : 0.008 0.080 2491 Dihedral : 16.228 90.143 5501 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.82 % Allowed : 16.03 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.15), residues: 1755 helix: -2.32 (0.11), residues: 1153 sheet: -2.33 (0.63), residues: 60 loop : -2.49 (0.22), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 171 HIS 0.005 0.001 HIS D 251 PHE 0.019 0.002 PHE C 192 TYR 0.022 0.002 TYR B 354 ARG 0.007 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8059 (mtmt) REVERT: A 599 GLU cc_start: 0.7332 (tt0) cc_final: 0.6836 (tm-30) REVERT: B 392 PHE cc_start: 0.7506 (t80) cc_final: 0.7254 (t80) REVERT: B 463 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7622 (pptt) REVERT: C 193 ASP cc_start: 0.8303 (t70) cc_final: 0.7982 (t0) REVERT: C 439 ARG cc_start: 0.7737 (mtm180) cc_final: 0.7376 (mtp85) REVERT: C 524 GLU cc_start: 0.7288 (tp30) cc_final: 0.7054 (tp30) REVERT: C 563 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.5493 (mtp85) REVERT: D 352 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7201 (mtt90) REVERT: D 443 ASP cc_start: 0.8451 (t0) cc_final: 0.8240 (t0) REVERT: D 453 ASN cc_start: 0.8425 (m-40) cc_final: 0.8012 (m110) REVERT: D 497 ASP cc_start: 0.7679 (t0) cc_final: 0.7418 (t0) outliers start: 13 outliers final: 7 residues processed: 212 average time/residue: 0.3024 time to fit residues: 91.0540 Evaluate side-chains 173 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 456 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 276 ASN A 405 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN B 196 GLN B 237 ASN B 317 ASN B 345 HIS B 422 GLN B 447 ASN B 484 GLN C 248 GLN C 299 ASN C 567 ASN C 604 GLN D 230 ASN D 232 ASN D 276 GLN ** D 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS D 365 HIS D 367 ASN D 426 ASN D 453 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN D 630 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 14941 Z= 0.156 Angle : 0.506 7.365 20284 Z= 0.268 Chirality : 0.039 0.153 2309 Planarity : 0.005 0.062 2491 Dihedral : 6.072 58.818 2085 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.01 % Allowed : 19.23 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 1755 helix: -0.29 (0.14), residues: 1167 sheet: -1.64 (0.65), residues: 55 loop : -1.87 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.018 0.001 PHE C 413 TYR 0.013 0.001 TYR B 357 ARG 0.002 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6158 (OUTLIER) cc_final: 0.4206 (t80) REVERT: A 344 GLU cc_start: 0.7044 (tp30) cc_final: 0.6790 (tt0) REVERT: A 391 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.5478 (mp) REVERT: A 448 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8059 (mtmt) REVERT: A 599 GLU cc_start: 0.7502 (tt0) cc_final: 0.7047 (tm-30) REVERT: B 270 TYR cc_start: 0.5121 (OUTLIER) cc_final: 0.4395 (p90) REVERT: B 392 PHE cc_start: 0.7563 (t80) cc_final: 0.7300 (t80) REVERT: B 570 SER cc_start: 0.8640 (m) cc_final: 0.8203 (p) REVERT: C 193 ASP cc_start: 0.8250 (t70) cc_final: 0.7923 (t0) REVERT: C 426 PHE cc_start: 0.4770 (OUTLIER) cc_final: 0.4042 (t80) REVERT: C 549 GLU cc_start: 0.6645 (pt0) cc_final: 0.6073 (pt0) REVERT: D 443 ASP cc_start: 0.8506 (t0) cc_final: 0.8245 (t0) REVERT: D 497 ASP cc_start: 0.7782 (t0) cc_final: 0.7494 (t0) outliers start: 32 outliers final: 13 residues processed: 203 average time/residue: 0.2700 time to fit residues: 81.7007 Evaluate side-chains 184 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14941 Z= 0.331 Angle : 0.576 8.865 20284 Z= 0.302 Chirality : 0.043 0.160 2309 Planarity : 0.004 0.048 2491 Dihedral : 5.214 53.089 2060 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.89 % Allowed : 20.24 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1755 helix: 0.34 (0.15), residues: 1158 sheet: -1.20 (0.67), residues: 63 loop : -1.80 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 445 HIS 0.003 0.001 HIS C 473 PHE 0.015 0.002 PHE D 516 TYR 0.017 0.002 TYR B 352 ARG 0.009 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.4251 (t80) REVERT: A 344 GLU cc_start: 0.7149 (tp30) cc_final: 0.6775 (tt0) REVERT: A 391 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.5597 (mp) REVERT: A 448 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8104 (mtmt) REVERT: A 599 GLU cc_start: 0.7563 (tt0) cc_final: 0.7052 (tm-30) REVERT: B 270 TYR cc_start: 0.5017 (OUTLIER) cc_final: 0.4213 (p90) REVERT: B 392 PHE cc_start: 0.7843 (t80) cc_final: 0.7424 (t80) REVERT: B 570 SER cc_start: 0.8779 (m) cc_final: 0.8498 (p) REVERT: C 426 PHE cc_start: 0.4815 (OUTLIER) cc_final: 0.4139 (t80) REVERT: D 443 ASP cc_start: 0.8532 (t0) cc_final: 0.8285 (t0) REVERT: D 497 ASP cc_start: 0.7940 (t0) cc_final: 0.7654 (t0) outliers start: 46 outliers final: 29 residues processed: 199 average time/residue: 0.2670 time to fit residues: 79.5962 Evaluate side-chains 191 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 0.0980 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 169 optimal weight: 0.0570 chunk 83 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 422 GLN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN D 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 14941 Z= 0.141 Angle : 0.471 9.073 20284 Z= 0.245 Chirality : 0.038 0.144 2309 Planarity : 0.003 0.040 2491 Dihedral : 4.672 51.988 2060 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.77 % Allowed : 21.31 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1755 helix: 1.02 (0.15), residues: 1157 sheet: -1.05 (0.67), residues: 63 loop : -1.53 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.004 0.001 HIS B 473 PHE 0.022 0.001 PHE C 413 TYR 0.012 0.001 TYR B 352 ARG 0.003 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.4820 (t80) REVERT: A 344 GLU cc_start: 0.6947 (tp30) cc_final: 0.6733 (tt0) REVERT: A 448 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8074 (mtmm) REVERT: A 599 GLU cc_start: 0.7488 (tt0) cc_final: 0.7077 (tm-30) REVERT: B 270 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.4292 (p90) REVERT: B 392 PHE cc_start: 0.7621 (t80) cc_final: 0.7263 (t80) REVERT: B 570 SER cc_start: 0.8721 (m) cc_final: 0.8331 (p) REVERT: C 193 ASP cc_start: 0.8032 (t70) cc_final: 0.7686 (t0) REVERT: C 426 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.4041 (t80) REVERT: D 443 ASP cc_start: 0.8413 (t0) cc_final: 0.8212 (t0) REVERT: D 497 ASP cc_start: 0.7908 (t0) cc_final: 0.7623 (t0) outliers start: 44 outliers final: 26 residues processed: 206 average time/residue: 0.2673 time to fit residues: 82.3910 Evaluate side-chains 191 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14941 Z= 0.198 Angle : 0.488 8.030 20284 Z= 0.254 Chirality : 0.040 0.144 2309 Planarity : 0.003 0.037 2491 Dihedral : 4.559 51.276 2060 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.58 % Allowed : 22.06 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1755 helix: 1.21 (0.15), residues: 1158 sheet: -1.00 (0.68), residues: 63 loop : -1.47 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.018 0.001 PHE C 413 TYR 0.014 0.001 TYR B 508 ARG 0.005 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.4972 (t80) REVERT: A 448 LYS cc_start: 0.8269 (mtpp) cc_final: 0.8060 (mtmm) REVERT: A 599 GLU cc_start: 0.7540 (tt0) cc_final: 0.7091 (tm-30) REVERT: B 270 TYR cc_start: 0.5081 (OUTLIER) cc_final: 0.4286 (p90) REVERT: B 392 PHE cc_start: 0.7658 (t80) cc_final: 0.7275 (t80) REVERT: B 570 SER cc_start: 0.8809 (m) cc_final: 0.8488 (p) REVERT: C 193 ASP cc_start: 0.8027 (t70) cc_final: 0.7683 (t0) REVERT: C 426 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.4201 (t80) REVERT: D 279 ARG cc_start: 0.8334 (tmm-80) cc_final: 0.7938 (ttp-170) REVERT: D 405 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8200 (tt) REVERT: D 443 ASP cc_start: 0.8408 (t0) cc_final: 0.8194 (t0) REVERT: D 497 ASP cc_start: 0.7911 (t0) cc_final: 0.7626 (t0) outliers start: 41 outliers final: 31 residues processed: 199 average time/residue: 0.2776 time to fit residues: 82.1142 Evaluate side-chains 198 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14941 Z= 0.162 Angle : 0.470 8.008 20284 Z= 0.243 Chirality : 0.039 0.139 2309 Planarity : 0.003 0.036 2491 Dihedral : 4.363 51.440 2060 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.95 % Allowed : 22.06 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1755 helix: 1.45 (0.15), residues: 1150 sheet: -1.44 (0.68), residues: 58 loop : -1.25 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.021 0.001 PHE C 413 TYR 0.011 0.001 TYR B 352 ARG 0.004 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 170 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5097 (t80) REVERT: A 391 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.5500 (mp) REVERT: A 402 MET cc_start: 0.6579 (tpp) cc_final: 0.5743 (tmm) REVERT: A 448 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7886 (ptpp) REVERT: B 270 TYR cc_start: 0.5155 (OUTLIER) cc_final: 0.4413 (p90) REVERT: B 392 PHE cc_start: 0.7678 (t80) cc_final: 0.7270 (t80) REVERT: B 570 SER cc_start: 0.8789 (m) cc_final: 0.8459 (p) REVERT: C 193 ASP cc_start: 0.7991 (t70) cc_final: 0.7670 (t0) REVERT: C 426 PHE cc_start: 0.5089 (OUTLIER) cc_final: 0.4142 (t80) REVERT: D 279 ARG cc_start: 0.8324 (tmm-80) cc_final: 0.7945 (ttp-170) REVERT: D 424 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 497 ASP cc_start: 0.7910 (t0) cc_final: 0.7644 (t0) outliers start: 47 outliers final: 34 residues processed: 199 average time/residue: 0.2671 time to fit residues: 78.2589 Evaluate side-chains 205 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14941 Z= 0.193 Angle : 0.486 8.518 20284 Z= 0.252 Chirality : 0.039 0.145 2309 Planarity : 0.003 0.035 2491 Dihedral : 4.336 51.431 2060 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.02 % Allowed : 22.06 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1755 helix: 1.49 (0.15), residues: 1149 sheet: -1.44 (0.68), residues: 58 loop : -1.20 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.019 0.001 PHE B 426 TYR 0.014 0.001 TYR B 352 ARG 0.005 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5117 (t80) REVERT: A 391 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.5550 (mp) REVERT: A 402 MET cc_start: 0.6578 (tpp) cc_final: 0.5722 (tmm) REVERT: A 448 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7883 (ptpp) REVERT: B 270 TYR cc_start: 0.5139 (OUTLIER) cc_final: 0.4380 (p90) REVERT: B 392 PHE cc_start: 0.7676 (t80) cc_final: 0.7251 (t80) REVERT: B 499 ARG cc_start: 0.6933 (ttp80) cc_final: 0.6730 (ptm160) REVERT: B 570 SER cc_start: 0.8790 (m) cc_final: 0.8508 (p) REVERT: C 426 PHE cc_start: 0.5061 (OUTLIER) cc_final: 0.4288 (t80) REVERT: C 603 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6699 (tpm170) REVERT: D 405 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8192 (tt) REVERT: D 424 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8434 (tp) REVERT: D 497 ASP cc_start: 0.7924 (t0) cc_final: 0.7685 (t0) outliers start: 48 outliers final: 35 residues processed: 204 average time/residue: 0.3071 time to fit residues: 92.5591 Evaluate side-chains 208 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 114 optimal weight: 0.2980 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14941 Z= 0.152 Angle : 0.471 9.337 20284 Z= 0.241 Chirality : 0.038 0.136 2309 Planarity : 0.003 0.035 2491 Dihedral : 4.180 51.800 2060 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.64 % Allowed : 22.44 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1755 helix: 1.64 (0.15), residues: 1150 sheet: -1.52 (0.65), residues: 60 loop : -1.09 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 445 HIS 0.004 0.001 HIS D 293 PHE 0.017 0.001 PHE B 426 TYR 0.011 0.001 TYR B 352 ARG 0.005 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5244 (t80) REVERT: A 344 GLU cc_start: 0.7133 (tp30) cc_final: 0.6759 (tt0) REVERT: A 391 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.5589 (mp) REVERT: A 402 MET cc_start: 0.6500 (tpp) cc_final: 0.5719 (tmm) REVERT: A 448 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7851 (ptpp) REVERT: B 270 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4388 (p90) REVERT: B 392 PHE cc_start: 0.7671 (t80) cc_final: 0.7271 (t80) REVERT: B 570 SER cc_start: 0.8762 (m) cc_final: 0.8460 (p) REVERT: C 193 ASP cc_start: 0.7901 (t70) cc_final: 0.7598 (t0) REVERT: C 426 PHE cc_start: 0.5122 (OUTLIER) cc_final: 0.4200 (t80) REVERT: C 439 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7424 (mtp180) REVERT: D 405 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8172 (tt) REVERT: D 424 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8425 (tp) REVERT: D 497 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) outliers start: 42 outliers final: 31 residues processed: 209 average time/residue: 0.2693 time to fit residues: 82.9392 Evaluate side-chains 205 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.0060 chunk 147 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14941 Z= 0.159 Angle : 0.475 9.230 20284 Z= 0.245 Chirality : 0.039 0.169 2309 Planarity : 0.003 0.054 2491 Dihedral : 4.153 52.075 2060 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.77 % Allowed : 22.31 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1755 helix: 1.65 (0.15), residues: 1150 sheet: -1.43 (0.65), residues: 60 loop : -0.99 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.024 0.001 PHE C 413 TYR 0.011 0.001 TYR B 352 ARG 0.006 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 171 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.5235 (t80) REVERT: A 344 GLU cc_start: 0.7146 (tp30) cc_final: 0.6767 (tt0) REVERT: A 402 MET cc_start: 0.6502 (tpp) cc_final: 0.5721 (tmm) REVERT: A 448 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7851 (ptpp) REVERT: B 270 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.4405 (p90) REVERT: B 392 PHE cc_start: 0.7670 (t80) cc_final: 0.7263 (t80) REVERT: B 414 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: B 570 SER cc_start: 0.8766 (m) cc_final: 0.8461 (p) REVERT: C 193 ASP cc_start: 0.7909 (t70) cc_final: 0.7584 (t0) REVERT: C 426 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.4268 (t80) REVERT: C 439 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7426 (mtp180) REVERT: C 577 PHE cc_start: 0.8564 (m-10) cc_final: 0.8292 (m-10) REVERT: D 405 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8170 (tt) REVERT: D 424 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8417 (tp) REVERT: D 497 ASP cc_start: 0.7921 (t0) cc_final: 0.7682 (t0) outliers start: 44 outliers final: 32 residues processed: 203 average time/residue: 0.2693 time to fit residues: 81.7592 Evaluate side-chains 207 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.1980 chunk 110 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14941 Z= 0.141 Angle : 0.477 9.268 20284 Z= 0.244 Chirality : 0.038 0.161 2309 Planarity : 0.003 0.041 2491 Dihedral : 3.895 52.225 2057 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.58 % Allowed : 22.50 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1755 helix: 1.74 (0.15), residues: 1148 sheet: -0.79 (0.68), residues: 55 loop : -0.90 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.030 0.001 PHE C 413 TYR 0.010 0.001 TYR B 352 ARG 0.006 0.000 ARG B 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5227 (t80) REVERT: A 344 GLU cc_start: 0.7132 (tp30) cc_final: 0.6794 (tt0) REVERT: A 402 MET cc_start: 0.6471 (tpp) cc_final: 0.5713 (tmm) REVERT: B 270 TYR cc_start: 0.5203 (OUTLIER) cc_final: 0.4398 (p90) REVERT: B 392 PHE cc_start: 0.7616 (t80) cc_final: 0.7219 (t80) REVERT: B 414 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: B 570 SER cc_start: 0.8730 (m) cc_final: 0.8413 (p) REVERT: C 193 ASP cc_start: 0.7769 (t70) cc_final: 0.7491 (t0) REVERT: C 439 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7420 (mtp180) REVERT: C 577 PHE cc_start: 0.8556 (m-10) cc_final: 0.8287 (m-10) REVERT: D 352 ARG cc_start: 0.7344 (mtt90) cc_final: 0.7105 (mtt90) REVERT: D 405 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8174 (tt) REVERT: D 424 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8431 (tp) REVERT: D 497 ASP cc_start: 0.7909 (t0) cc_final: 0.7682 (t0) outliers start: 41 outliers final: 34 residues processed: 201 average time/residue: 0.2684 time to fit residues: 81.1267 Evaluate side-chains 208 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 128 optimal weight: 0.6980 chunk 20 optimal weight: 0.0570 chunk 38 optimal weight: 0.0270 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 567 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.200214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155367 restraints weight = 20293.189| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 4.83 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14941 Z= 0.132 Angle : 0.470 9.301 20284 Z= 0.240 Chirality : 0.038 0.148 2309 Planarity : 0.003 0.037 2491 Dihedral : 3.810 52.601 2057 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.26 % Allowed : 23.07 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1755 helix: 1.86 (0.15), residues: 1148 sheet: -0.68 (0.69), residues: 55 loop : -0.83 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 PHE 0.027 0.001 PHE C 413 TYR 0.009 0.001 TYR A 546 ARG 0.005 0.000 ARG B 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2944.66 seconds wall clock time: 54 minutes 29.40 seconds (3269.40 seconds total)